R J Roberts

Summary

Affiliation: New England Biolabs
Country: USA

Publications

  1. pmc Genomic functional annotation using co-evolution profiles of gene clusters
    Yu Zheng
    Bioinformatics Graduate Program, Boston University, Boston, MA 02215, USA
    Genome Biol 3:RESEARCH0060. 2002
  2. pmc Identifying protein function--a call for community action
    Richard J Roberts
    New England Biolabs, located in Beverly, Massachusetts, USA
    PLoS Biol 2:E42. 2004
  3. pmc REBASE--restriction enzymes and DNA methyltransferases
    Richard J Roberts
    New England Biolabs, Inc, 32 Tozer Road, Beverly, MA 01915 USA
    Nucleic Acids Res 33:D230-2. 2005
  4. pmc REBASE--a database for DNA restriction and modification: enzymes, genes and genomes
    Richard J Roberts
    New England Biolabs, Inc, 240 County Road, Ipswich, MA 01938, USA
    Nucleic Acids Res 38:D234-6. 2010
  5. pmc The BsaHI restriction-modification system: cloning, sequencing and analysis of conserved motifs
    Robert K Neely
    School of Chemistry, The University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, UK
    BMC Mol Biol 9:48. 2008
  6. pmc A genetic dissection of the LlaJI restriction cassette reveals insights on a novel bacteriophage resistance system
    Jonathan O'Driscoll
    Department of Microbiology, University College Cork, Cork, Ireland
    BMC Microbiol 6:40. 2006
  7. pmc Phylogenetic detection of conserved gene clusters in microbial genomes
    Yu Zheng
    Bioinformatics Graduate Program, Boston University, Boston, MA, USA
    BMC Bioinformatics 6:243. 2005
  8. pmc REBASE-restriction enzymes and methylases
    R J Roberts
    New England Biolabs, 32 Tozer Road, Beverly, MA 01915, USA
    Nucleic Acids Res 25:248-62. 1997
  9. pmc REBASE: restriction enzymes and methyltransferases
    Richard J Roberts
    New England Biolabs, Inc, 32 Tozer Road, Beverly, MA 01915, USA
    Nucleic Acids Res 31:418-20. 2003
  10. pmc How restriction enzymes became the workhorses of molecular biology
    Richard J Roberts
    New England Biolabs, 32 Tozer Road, Beverly, MA 01915, USA
    Proc Natl Acad Sci U S A 102:5905-8. 2005

Detail Information

Publications46

  1. pmc Genomic functional annotation using co-evolution profiles of gene clusters
    Yu Zheng
    Bioinformatics Graduate Program, Boston University, Boston, MA 02215, USA
    Genome Biol 3:RESEARCH0060. 2002
    ..The gene cluster phylogenetic profile integrates chromosomal proximity information and phylogenetic profile information and allows us to infer functional dependences between the gene clusters even at great distance on the chromosome...
  2. pmc Identifying protein function--a call for community action
    Richard J Roberts
    New England Biolabs, located in Beverly, Massachusetts, USA
    PLoS Biol 2:E42. 2004
  3. pmc REBASE--restriction enzymes and DNA methyltransferases
    Richard J Roberts
    New England Biolabs, Inc, 32 Tozer Road, Beverly, MA 01915 USA
    Nucleic Acids Res 33:D230-2. 2005
    ..The contents of REBASE are available by browsing from the web (http://rebase.neb.com/rebase/rebase.html) and through selected compilations by ftp (ftp.neb.com) and as monthly updates that can be requested via email...
  4. pmc REBASE--a database for DNA restriction and modification: enzymes, genes and genomes
    Richard J Roberts
    New England Biolabs, Inc, 240 County Road, Ipswich, MA 01938, USA
    Nucleic Acids Res 38:D234-6. 2010
    ..The contents of REBASE may be browsed from the web (http://rebase.neb.com) and selected compilations can be downloaded by ftp (ftp.neb.com). Additionally, monthly updates can be requested via email...
  5. pmc The BsaHI restriction-modification system: cloning, sequencing and analysis of conserved motifs
    Robert K Neely
    School of Chemistry, The University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, UK
    BMC Mol Biol 9:48. 2008
    ..Understanding the mechanism of this recognition represents a significant challenge that we begin to address for the BsaHI restriction-modification system, which recognises the six base sequence GRCGYC...
  6. pmc A genetic dissection of the LlaJI restriction cassette reveals insights on a novel bacteriophage resistance system
    Jonathan O'Driscoll
    Department of Microbiology, University College Cork, Cork, Ireland
    BMC Microbiol 6:40. 2006
    ..LlaJI and R2.LlaJI). Here we employ a detailed genetic analysis of the LlaJI restriction determinants in an attempt to characterize mechanistic features of this unusual hetero-oligomeric endonuclease...
  7. pmc Phylogenetic detection of conserved gene clusters in microbial genomes
    Yu Zheng
    Bioinformatics Graduate Program, Boston University, Boston, MA, USA
    BMC Bioinformatics 6:243. 2005
    ....
  8. pmc REBASE-restriction enzymes and methylases
    R J Roberts
    New England Biolabs, 32 Tozer Road, Beverly, MA 01915, USA
    Nucleic Acids Res 25:248-62. 1997
    ..neb.com/rebase ). Specialized files are available that can be used directly by many software packages...
  9. pmc REBASE: restriction enzymes and methyltransferases
    Richard J Roberts
    New England Biolabs, Inc, 32 Tozer Road, Beverly, MA 01915, USA
    Nucleic Acids Res 31:418-20. 2003
    ..The data is available on the web (http://rebase.neb.com/rebase/rebase.html), through ftp (ftp.neb.com) and as monthly updates via email...
  10. pmc How restriction enzymes became the workhorses of molecular biology
    Richard J Roberts
    New England Biolabs, 32 Tozer Road, Beverly, MA 01915, USA
    Proc Natl Acad Sci U S A 102:5905-8. 2005
    ..This pioneering study set the stage for the modern practice of molecular biology in which restriction enzymes are ubiquitous tools, although they are often taken for granted...
  11. pmc A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes
    Richard J Roberts
    New England Biolabs, Beverly, MA 01915, USA
    Nucleic Acids Res 31:1805-12. 2003
    ..It provides explicit categories for the many different Type II enzymes now identified and provides a system for naming the putative genes found by sequence analysis of microbial genomes...
  12. pmc REBASE--enzymes and genes for DNA restriction and modification
    Richard J Roberts
    New England Biolabs Inc, 240 County Road, Ipswich, MA 01938, USA
    Nucleic Acids Res 35:D269-70. 2007
    ..The contents or REBASE may be browsed from the web (http://rebase.neb.com/rebase/rebase.ftp.html) and selected compilations can be downloaded by ftp (ftp.neb.com). Additionally, monthly updates can be requested via email...
  13. pmc COMBREX: COMputational BRidge to EXperiments
    Richard J Roberts
    New England Biolabs, 240 County Road, Ipswich, MA 01938, USA
    Biochem Soc Trans 39:581-3. 2011
    ..A pilot project is running that focuses on bacterial and archaeal genomes...
  14. pmc REBASE--restriction enzymes and methylases
    R J Roberts
    New England Biolabs, 32 Tozer Road, Beverly, MA 01915, USA
    Nucleic Acids Res 29:268-9. 2001
    ..The data is distributed via email, ftp (ftp.neb.com) and the Web (http://rebase. neb.com)...
  15. ncbi request reprint The early days of bioinformatics publishing
    R J Roberts
    New England Biolabs, Beverly, MA 01915, USA
    Bioinformatics 16:2-4. 2000
    ..A brief history of the early days of publishing in the bioinformatics field is presented...
  16. pmc REBASE - restriction enzymes and methylases
    R J Roberts
    New England Biolabs, Inc, 32 Tozer Road, Beverly, MA 01915, USA
    Nucleic Acids Res 28:306-7. 2000
    ..Most recently, putative DNA methyltransferases and restriction enzymes, as predicted from analysis of genomic sequences, are also listed. The data is distributed via Email, ftp (ftp.neb.com), and the Web (http://rebase.neb.com)...
  17. pmc REBASE-restriction enzymes and methylases
    R J Roberts
    New England Biolabs, 32 Tozer Road, Beverly, MA 01915, USA
    Nucleic Acids Res 27:312-3. 1999
    ..Additionally, there is a search facility, help and NEWS pages, and a complete description of our various services. Specialized files are available that can be used directly by many software packages...
  18. ncbi request reprint Base flipping
    R J Roberts
    New England Biolabs, Beverly, Massachusetts 01915, USA
    Annu Rev Biochem 67:181-98. 1998
    ..This review describes systems known to use base flipping as well as many systems where it is likely to occur but has not yet been rigorously demonstrated. The mechanism and evolution of base flipping are also discussed...
  19. pmc REBASE - restriction enzymes and methylases
    R J Roberts
    New England Biolabs, 32 Tozer Road, Beverly, MA 01915, USA
    Nucleic Acids Res 26:338-50. 1998
    ..Additionally, there is a search facility, help and NEWS pages, and a complete description of our various services. Specialized files are available that can be used directly by many software packages...
  20. pmc COMBREX: a project to accelerate the functional annotation of prokaryotic genomes
    Richard J Roberts
    Bioinformatics Program, Boston University, Boston, MA 02215, USA
    Nucleic Acids Res 39:D11-4. 2011
    ..It consists of a database of functional predictions produced by computational biologists and a mechanism for experimental biochemists to bid for the validation of those predictions. Small grants are available to support successful bids...
  21. pmc Functional analysis of putative restriction-modification system genes in the Helicobacter pylori J99 genome
    H Kong
    New England Biolabs, 32 Tozer Road, Beverly, MA 01915, USA
    Nucleic Acids Res 28:3216-23. 2000
    ..Helicobacter pylori may maintain a variety of functional R-M systems, which are believed to be a primitive bacterial 'immune' system, by alternatively turning on/off a subset of numerous R-M systems...
  22. pmc NEBcutter: A program to cleave DNA with restriction enzymes
    Tamas Vincze
    New England Biolabs, Inc, 32 Tozer Road, Beverly, MA 01915, USA
    Nucleic Acids Res 31:3688-91. 2003
    ..Many options exist to choose the enzymes used for digestion, including all known specificities, subsets of those that are commercially available or sets of enzymes that produce compatible termini...
  23. pmc Segmentally variable genes: a new perspective on adaptation
    Yu Zheng
    Bioinformatics Graduate Program, Boston University, Boston, Massachusetts, USA
    PLoS Biol 2:E81. 2004
    ..Discerning their function and identifying their binding partners may offer biologists new insights into the basic mechanisms of adaptation, context-dependent evolution, and the interaction between microbes and their environment...
  24. pmc Two crystal forms of the restriction enzyme MspI-DNA complex show the same novel structure
    Qian Steven Xu
    Department of Physiology and Biophysics, Boston University School of Medicine, Boston, MA 02118, USA
    Protein Sci 14:2590-600. 2005
    ..Combined with structural information from other solved structures of Type II restriction enzymes, the possible relationship between the structures of the enzymes and their cleavage behaviors is discussed...
  25. pmc DNA containing 4'-thio-2'-deoxycytidine inhibits methylation by HhaI methyltransferase
    S Kumar
    New England Biolabs, 32 Tozer Road, Beverly, MA 01915, USA
    Nucleic Acids Res 25:2773-83. 1997
    ..This inhibitory effect can be partially overcome after a considerably long time in the crystal environment where the packing prevents complex dissociation and the target is accurately positioned within the active site...
  26. pmc Comparative genomics of the restriction-modification systems in Helicobacter pylori
    L F Lin
    New England Biolabs, Inc, 32 Tozer Road, Beverly, MA 01915, USA
    Proc Natl Acad Sci U S A 98:2740-5. 2001
    ..Our results also show that H. pylori has extremely diversified R-M systems in different strains, and that the diversity may be maintained by constantly acquiring new R-M systems and by inactivating and deleting the old ones...
  27. pmc Selection of restriction endonucleases using artificial cells
    Yu Zheng
    New England Biolabs, Inc, 240 County Road, Ipswich, MA 01938, USA
    Nucleic Acids Res 35:e83. 2007
    ..manalii. This method provides a unique tool for cloning restriction endonuclease genes and has many other potential applications...
  28. pmc Characterization of two new aminopeptidases in Escherichia coli
    Yu Zheng
    Bioinformatics Graduate Program, Boston University, Massachusetts 02215, USA
    J Bacteriol 187:3671-7. 2005
    ..ypdE is the immediate downstream gene of ypdF, and its start codon overlaps with the stop codon of ypdF by 1 base. YpdE is shown to be a metalloaminopeptidase and has a broad exoaminopeptidase activity...
  29. pmc Identification of genes with fast-evolving regions in microbial genomes
    Yu Zheng
    Bioinformatics Graduate Program, Boston University, Boston, MA 02215, USA
    Nucleic Acids Res 32:6347-57. 2004
    ..Gene sets reported from our method provide a measure of the phenotypic divergence between two closely related genomes...
  30. pmc A unique family of Mrr-like modification-dependent restriction endonucleases
    Yu Zheng
    New England Biolabs, Inc, 240 County Road, Ipswich, MA, 01938, USA
    Nucleic Acids Res 38:5527-34. 2010
    ..The MspJI enzyme family, with their different recognition specificities and cleavage properties, provides a basis on which many future methods can build to decode the epigenomes of different organisms...
  31. pmc Functional characterization of the YmcB and YqeV tRNA methylthiotransferases of Bacillus subtilis
    Brian P Anton
    New England Biolabs, Ipswich, MA 01938, USA
    Nucleic Acids Res 38:6195-205. 2010
    ..Finally, we performed a computational analysis to identify candidate residues outside the TRAM domain that may be involved with substrate recognition. These residues represent interesting targets for further analysis...
  32. pmc Computational identification of operons in microbial genomes
    Yu Zheng
    Bioinformatics Graduate Program, Boston University, Boston, Massachusetts 02215, USA
    Genome Res 12:1221-30. 2002
    ..We looked further into the conservation of operons across genomes. A trp operon alignment is analyzed in depth to show gene loss and rearrangement in different organisms during operon evolution...
  33. pmc Using shotgun sequence data to find active restriction enzyme genes
    Yu Zheng
    New England Biolabs, Inc, 240 County Road, Ipswich, MA 01938, USA
    Nucleic Acids Res 37:e1. 2009
    ..Active restriction enzyme genes have been identified, and their activity demonstrated biochemically, in the sequenced genomes of Methanocaldococcus jannaschii, Bacillus cereus ATCC 10987 and Methylococcus capsulatus...
  34. pmc RimO, a MiaB-like enzyme, methylthiolates the universally conserved Asp88 residue of ribosomal protein S12 in Escherichia coli
    Brian P Anton
    New England Biolabs, Ipswich, MA 01938, USA
    Proc Natl Acad Sci U S A 105:1826-31. 2008
    ..The initial results presented here constitute a bioinformatics-driven prediction with preliminary experimental validation that should serve as the starting point for several interesting lines of further inquiry...
  35. pmc Co-operation and communication between the human maintenance and de novo DNA (cytosine-5) methyltransferases
    Gun Do Kim
    New England Biolabs, 32 Tozer Road, Beverly, MA 01915, USA
    EMBO J 21:4183-95. 2002
    ..In vivo co-expression of hDNMT1 and hDNMT3a or hDNMT3b leads to methylation spreading in the genome, suggesting co-operation between de novo and maintenance enzymes during DNA methylation...
  36. pmc The human proteins MBD5 and MBD6 associate with heterochromatin but they do not bind methylated DNA
    Sophie Laget
    New England Biolabs, Ipswich, Massachusetts, United States of America
    PLoS ONE 5:e11982. 2010
    ..It is unknown whether MBD5 or MBD6 also bind methylated DNA; this question has interest for basic research, but also practical consequences for human health, as MBD5 deletions are the likely cause of certain cases of mental retardation...
  37. pmc Baculovirus-mediated expression and characterization of the full-length murine DNA methyltransferase
    S Pradhan
    New England Biolabs, 32 Tozer Road, Beverly, MA 01915, USA
    Nucleic Acids Res 25:4666-73. 1997
    ..The new clones are capable of yielding large quantities of intact MTases for further structural and functional studies...
  38. pmc Structure of HinP1I endonuclease reveals a striking similarity to the monomeric restriction enzyme MspI
    Zhe Yang
    Department of Biochemistry, Emory University School of Medicine 1510 Clifton Road, Atlanta, GA 30322, USA
    Nucleic Acids Res 33:1892-901. 2005
    ..A possible functional link between this unusual dimerization mode and the tetrameric restriction enzymes is discussed...
  39. pmc DNA nicking by HinP1I endonuclease: bending, base flipping and minor groove expansion
    John R Horton
    Department of Biochemistry, Emory University School of Medicine 1510 Clifton Road, Atlanta, GA 30322, USA
    Nucleic Acids Res 34:939-48. 2006
    ....
  40. pmc Identification of GATC- and CCGG-recognizing Type II REases and their putative specificity-determining positions using Scan2S--a novel motif scan algorithm with optional secondary structure constraints
    Masha Y Niv
    Department of Physiology and Biophysics, Weill Medical College of Cornell University, 1300 York Ave, New York, New York 10021, USA
    Proteins 71:631-40. 2008
    ..The new motifs highlight potential specificity-determining positions that do not fully overlap for the GATC- and the CCGG-recognizing REases and are candidates for specificity re-engineering...
  41. pmc Structural characterization and comparative phylogenetic analysis of Escherichia coli HemK, a protein (N5)-glutamine methyltransferase
    Zhe Yang
    Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, USA
    J Mol Biol 340:695-706. 2004
    ..Comparative phylogenetic analysis of the hemK gene and its frequent neighbor gene, prfA, which encodes a major substrate, provides evidence for several examples of lateral gene transfer...
  42. ncbi request reprint An asymmetric complex of restriction endonuclease MspI on its palindromic DNA recognition site
    Qian Steven Xu
    Department of Physiology and Biophysics, Boston University School of Medicine, 715 Albany Street, MA 02118, USA
    Structure 12:1741-7. 2004
    ..A few possible pathways are discussed for MspI to cut both strands of DNA, either as a monomer or dimer...
  43. ncbi request reprint Preserving an important collection
    Norton Zinder
    Science 307:519. 2005
  44. ncbi request reprint Save your notes, drafts and printouts: today's work is tomorrow's history
    Sydney Brenner
    Nature 446:725. 2007
  45. ncbi request reprint Richard J. Roberts--Nobel Laureate for discovery of split genes
    Marc A Shampo
    Mayo Clin Proc 78:132. 2003
  46. ncbi request reprint Structure of the Q237W mutant of HhaI DNA methyltransferase: an insight into protein-protein interactions
    Aiping Dong
    Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, USA
    Biol Chem 385:373-9. 2004
    ..A possible evolutionary link between the Type I and Type II restriction-modification systems is discussed...